Sequence
atgc intronic sequence ATGC exonic sequence...tggttcaatttaaggaatgaataatcaaggataaaatgctgaaattctgtgttgttatgtggctgatgcatattctgtcttttcaatttgttgtctgcagTGGGTTTTGTCTTCTAAGGAAATTAACTTCCCTTATCCTTTGGGGTTGACTCTACTTCACATGGTCTTCTCCTCTGTTCTGTGTTTTGTGTTAACCAAGA
Basic information
species | Glycine max |
transcript | GLYMA08G18730.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G18730.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G53660.1 (Arabidopsis thaliana), 3'ss of exon 1
tggttcaatttaaggaatgaataatcaaggataaaatgctgaaattctgtgttgttatgtggctgatgca-tattctgtcttttcaatttgttgtc-tgcagTGGGTTTTGTCTTCTAAGGAAATTAACTTCCCTTATCCTTTGGGGTTGACTCTACTTCACATGGTCTTCTCCTCTGTTCTGTGTTTTGTGTTAACCAAGA
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--ttcaaacttttgtaaattttggttcattccatttctctttagcttctttcagtttcttttttccagcactaatttttatttctgactcaatctgatgcagTGGGTATTGTCATCTAAGGAAATAAACTTCCCTTATCCACTTGGATTGACATTACTTCACATGACTTTTTCCTCTGTTTTGTGTTTTCTCCTCACGAAGG
upper sequence: GLYMA08G18730.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G14410.1 (Arabidopsis thaliana), 3'ss of exon 1
-----tggttcaatttaaggaatgaataatcaaggataaaatgctgaaattctgtgttgttatgtggctgatgcatattctgtcttttcaatttgttgtctgcagTGGGTTTTGTCTTCTAAGGAAATTAACTTCCCTTATCCTTTGGGGTTGACTCTACTTCACATGGTCTTCTCCTCTGTTCTGTGTTTTGTGTTAACCAAGA
| || | | | | | ||| | ||| | || | ||| | || | || || | | || ||||||| |||| | ||||||||||||||||| |||||||||||||| |||||||||||| | || |||||| |||| || ||| |||| |||||||| |||| ||| | | |||||
ttcaccgttttacaatctgtagcaagtaacgattcatagattgtggtttctctcttttcgt-catgactaacgt---ttttgtctttg-aattgctctgctgcagTGGGTTTTGTCATCTAAGGAAATTAATTTCCCTTATCCTCTTGGATTGACTTTACTCCATATGATCTTTTCCTCTGTCTTGTGCTTTCTTCTTACCAAAG
upper sequence: GLYMA08G18730.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv15s0046g00460.t01 (Vitis vinifera), 3'ss of exon 1
---tggttcaatttaaggaatgaataatcaaggataaaa-tgctgaaattctgtgttgttatgtggctgatgcatattctgtcttttcaatttgttgtctgcagTGGGTTTTGTCTTCTAAGGAAATTAACTTCCCTTATCCTTTGGGGTTGACTCTACTTCACATGGTCTTCTCCTCTGTTCTGTGTTTTGTGTTAACCAAGA
| || || | | | ||| |||| || | | | || | | ||||| | || | | |||| | || |||| || ||||||||||||| || |||||||| || ||||| || || | || ||||||| ||||||||||||||||||||||| |||| ||| | | ||||
tttttttttttctttacctctctcttatccttgatatctctgtttgagctttgcttc---acatggctaacagatgattt-tcttctaaaattgtaaaatgtagTGGGTTTTGTCATCAAAGGAAATAAATTTCCCCTACCCACTTGGACTGACTCTGCTTCACATGGTCTTCTCCTCTGTATTGTGCTTTATTCTCACCAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgtgttgttatgtggctgatgcatattctgtcttttcaatttgttgtctgcagTGGGTTTTGTCTTCTAAGGAAATTAACTTCCCTTATCCTTTGGGGTTGACTCTACTTCACATGGTCTTCTCCTCTGTTCTGTGTTTTGTGTTAACCAAGA
ggctgat putative branch site (score: 4)
ttttcaattt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggttcaatttaaggaatgaataatcaaggataaaatgctgaaattctgtgttgttatgtggctgatgcatattctgtcttttcaatttgttgtctgcagTGGGTTTTGTCTTCTAAGGAAATTAACTTCCCTTATCCTTTGGGGTTGACTCTACTTCACATGGTCTTCTCCTCTGTTCTGTGTTTTGTGTTAACCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - -ggaatga
- - - - - - - - - - - - - - ggataaaa
- - - - - - - - - - - - - - - - - - tgctgaa
- - - - - - - - - - - - - - - - - - - - - - ttctgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - tgttatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgatgc